VEP Polaris 🌟

VEP Polaris Documentation Site

A lightweight toolkit to inspect, validate, and manage plugin data for Ensembl Variant Effect Predictor (VEP).

VEP Polaris helps you navigate the complex ecosystem of Ensembl VEP plugin data files by ensuring compatibility, correctness, and clarity in your annotation pipeline.

Why Use VEP Polaris?

• Prevent silent or breaking VEP annotation errors due to chr1 vs 1 mismatches
• Test and validate plugin data structure before annotation
• Identify problematic or empty files in large plugin datasets
• Prepare and clean up custom plugin inputs

Tools Included

Command	Description
plugin-inspect	Scans plugin files for usable data and chromosome format consistency

Each command is a self-contained script, callable through the vep-polaris dispatcher.

Installation

git clone https://github.com/sblinde/vep-polaris.git
cd vep-polaris

🔧 Quick Install

If you have Node.js installed on your machine:

npm run install

This will:

• Make all CLI and test scripts executable
• Optionally symlink vep-polaris to /usr/local/bin
• Print documentation setup tips

⚠️ If you’re not using Node, you can still run:

chmod +x install.sh && ./install.sh

🧪 Run Tests

To validate that tools like plugin-inspect work as expected:

If you are using Node, you can run

npm test

or, otherwise:

./run-tests.sh

See docs/testing.md for more detail.

Usage

vep-polaris <command> [options]

Example:

vep-polaris plugin-inspect --dir /vep/Plugins

Run any command with --help for further details.

vep-polaris plugin-inspect --help

Project Structure

vep-polaris/
├── bin/                  # All subcommands and CLI dispatcher
│   ├── vep-polaris
│   ├── plugin-inspect
│   └── ...
├── docs/                 # Detailed command documentation
├── tests/                # Test scripts for tools
├── README.md
├── LICENSE
└── .gitignore

Working with Documentation

You can preview the docs/ folder using MKDocs.

npm run docs:serve     # Preview at http://localhost:8000

Contributing

At this time, this is a small side project owned by me, Sam Blinde as I endeavor in the world of bioinformatics. As this project may grow over time during my learning, I'd welcome the following support:

• Suggesting a new tool in this repo
• Submit a bug fix if you come across one
• Improving documentation or test coverage

License

This project is licensed under the MIT License. See LICENSE for details.

Acknowledgments ⭐

• Built with love by Sam Blinde.
• Inspired by wrestling with VEP plugin formats.
• Much appreciation to everyone who has contributed to Ensembl VEP and all of the plugins underneath it, for this little project would not exist without it.